standardDeviationOfTouchingNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the standard deviation value of touching neighbor labels. The radius of the neighborhood can be configured:

radius 0: Nothing is replaced
radius 1: direct neighbors are taken into account
radius 2: neighbors and neighbors or neighbors are taken into account
radius n: …

Note: Values of all pixels in a label each must be identical.

Parameters

parametric_map : Image label_map : Image parametric_map_destination : Image radius : int ignore_touching_background : bool

Returns

parametric_map_destination

Categories: Measurements, Filter, Graphs

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.

Usage in ImageJ macro

Ext.CLIJ2_standardDeviationOfTouchingNeighborsMap(Image parametric_map, Image label_map, Image parametric_map_destination, Number radius, Boolean ignore_touching_background);

Usage in object oriented programming languages

Java

// init CLIJ and GPU
import net.haesleinhuepf.clij2.CLIJ2;
import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
CLIJ2 clij2 = CLIJ2.getInstance();

// get input parameters
ClearCLBuffer parametric_map = clij2.push(parametric_mapImagePlus);
ClearCLBuffer label_map = clij2.push(label_mapImagePlus);
parametric_map_destination = clij2.create(parametric_map);
int radius = 10;
boolean ignore_touching_background = true;

// Execute operation on GPU
clij2.standardDeviationOfTouchingNeighborsMap(parametric_map, label_map, parametric_map_destination, radius, ignore_touching_background);

// show result
parametric_map_destinationImagePlus = clij2.pull(parametric_map_destination);
parametric_map_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(parametric_map);
clij2.release(label_map);
clij2.release(parametric_map_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
parametric_map = clij2.pushMat(parametric_map_matrix);
label_map = clij2.pushMat(label_map_matrix);
parametric_map_destination = clij2.create(parametric_map);
radius = 10;
ignore_touching_background = true;

% Execute operation on GPU
clij2.standardDeviationOfTouchingNeighborsMap(parametric_map, label_map, parametric_map_destination, radius, ignore_touching_background);

% show result
parametric_map_destination = clij2.pullMat(parametric_map_destination)

% cleanup memory on GPU
clij2.release(parametric_map);
clij2.release(label_map);
clij2.release(parametric_map_destination);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);

clij2 = CLICY.getInstance();

// get input parameters
parametric_map_sequence = getSequence();
parametric_map = clij2.pushSequence(parametric_map_sequence);
label_map_sequence = getSequence();
label_map = clij2.pushSequence(label_map_sequence);
parametric_map_destination = clij2.create(parametric_map);
radius = 10;
ignore_touching_background = true;

// Execute operation on GPU
clij2.standardDeviationOfTouchingNeighborsMap(parametric_map, label_map, parametric_map_destination, radius, ignore_touching_background);

// show result
parametric_map_destination_sequence = clij2.pullSequence(parametric_map_destination)
Icy.addSequence(parametric_map_destination_sequence);
// cleanup memory on GPU
clij2.release(parametric_map);
clij2.release(label_map);
clij2.release(parametric_map_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.standard_deviation_of_touching_neighbors_map(parametric_map, label_map, parametric_map_destination, radius, ignore_touching_background)

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